Rare Diseases services

Name Description ELIXIR Node
ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

 EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium, ELIXIR France, ELIXIR Denmark, ELIXIR Italy
ELIXIR Netherlands
ELIXIR France
ELIXIR Spain
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR France
ELIXIR France
ELIXIR France

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium, ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France

The ELIXIR Rare Disease (RD) community encompasses life science IT infrastructure developers, data scientists, and training experts within ELIXIR nodes who specifically target rare disease objectives. Associated are RD stakeholders who define overarching challenges for RD research, such as IRDiRC, ERNs, the EJP-RD, EURORDIS and patient organisations, and other infrastructures that serve the rare disease community, such as EOSC, INFRAFRONTIER, BBMRI, EATRIS or ECRIN.

The ELIXIR Rare Disease (RD) Community will continue to be committed to the International Rare Disease Research Consortium (IRDiRC) Vision for 2027: Enable all people living with a rare disease to receive an accurate diagnosis, care, and available therapy within one year of coming to medical attention.

To support such vision and facilitate data interoperability and analysis, the Community drives the assembly of service collections relevant for RD research, seeks interactions with other ELIXIR Human Data Communities to adapt and integrate resources and conducts Proof of Concept and pilot implementations of standards and methodologies.
OBJECTIVES

  • Coordinate and align RD research activities related to data resources, tools and services within ELIXIR and with other European and International activities.
  • Demonstrate the exploitation of FAIR data to reduce analytics complexity for data scientists
  • Consolidate the recently created ELIXIR RD Service Collections (former “Bundles”)
  • Disseminate and provide training on services and developments from the ELIXIR RD Community in collaboration with the ELIXIR Training Platform
 ELIXIR Spain, ELIXIR France, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Switzerland, ELIXIR Italy, ELIXIR UK, ELIXIR Belgium, ELIXIR Germany, ELIXIR Slovenia, ELIXIR Greece
ELIXIR Netherlands, ELIXIR Spain
ELIXIR Italy, ELIXIR Netherlands
ELIXIR Belgium, ELIXIR Denmark, ELIXIR Finland, ELIXIR France, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Spain, ELIXIR Sweden, EMBL-EBI

The FAIR (Findable, Accessible, Interoperable and Reusable) principles aim to maximize the discovery and reusability of digital resources. While the principles have enjoyed rapid uptake across communities (ELIXIR, G20, EOSC, H2020, NIH), the implementation details remain unclear.

Recently, we developed a prototype software infrastructure and a set of metrics to assess the FAIRness of digital resources (http://fairmetrics.org/). In this ELIXIR Implementation Study we will put these into practice for the ELIXIR community by starting to FAIRify ELIXIR Core Data Resources ArrayExpress, ENA, PDBe, PRIDE, CatH, CHEMBL, ChEBI, UNIPROT, HPA, INTERPRO, MINT, and STRING-db.

Our study will first establish effective guidelines for implementation, then involve hands-on FAIRification workshops, in which FAIRness will be assessed before and after the work done. Our work will raise awareness around what it takes to be FAIR, and to help drive interoperability between core ELIXIR resources and with efforts outside of ELIXIR.

 ELIXIR Netherlands, ELIXIR UK, EMBL-EBI, ELIXIR Italy, ELIXIR Sweden
ELIXIR France

In the process of establishing the functional consequences of putative or known genetic variants associated with disease, it is imperative to search worldwide resources and data for evidence already available. In the rare disease field, the challenges of doing this are pronounced as data are often fragmented as disease cohorts are small and managed by specialised researchers/physicians.

This study was designed to map out the requirements for making sources of data FAIR, with a particular focus on interoperability as well as enabling federated queries. The overall aim being to accelerate the functional interpretation of genetic variants.

The intention is that researchers and others working specifically on rare disease will benefit by the improved access to genoptype-phenotype data, recomended ontologies, evaluated tools and sources concerning: 

  • Rare disease pathways (WikiPathways)  
  • Drug development 
  • Drug target interactions (ChEMBL) 

The study has now finished: see the end report, and includes details of a number of papers, tools and datasets. This is a growing area with a great need for wider knowledge dissemination, training and building a standardised approach across clinicians and researchers. 

Webinar summarising the outcomes

(rec. Feb 2018) 

 

 ELIXIR Netherlands, ELIXIR Spain, ELIXIR Italy
ELIXIR Netherlands

This study is associated with the ongoing work of the Rare Disease Community.

Access to multiple biological and clinical resources without too many barriers is of critical importance in the rare diseases field. Because of the low frequency in the population, combining data across registries, biobanks, and -omics databases is the single most important way of finding materials and gaining new insights. 

This Rare Disease project was a joint initiative of the EU-funded RD-CONNECT project, BBMRI-NL, BBMRI-ERIC and ELIXIR. Its aim was to create a federated infrastructure that will enable access to different rare disease repositories across Europe. ELIXIR's role was to test different technologies for the interoperability backbone, which will feed into the rare disease use case within ELIXIR-EXCELERATE.

The study has now finished, the details are set out in the end report. 

Webinar summarising the outcomes

Other Implementation Studies:

 

 

 ELIXIR Netherlands, ELIXIR France, EMBL-EBI

This Study will build on recent developments across the RD community by aligning and securely interconnecting existing international infrastructures (RD-Connect, European Genome-phenome Archive (EGA), and tranSMART) with the general ELIXIR infrastructure. Tasks will develop upon services provided by ELIXIR Nodes and international standards such as those from the Global Alliance for Genomics and Health (GA4GH).

This proposal will also build on the FAIR metrics described by Wilkinson et al. to establish a framework for RD data FAIRification by providing RD-specific recommendations and FAIRness scores. This framework will be evaluated through the FAIRNess estimation of different key RD resources such as Orphanet and the RD-Connect platform. Once defined, the RD-adapted FAIR metrics will be prepared for IRDiRC recognition to serve the entire RD community.

The Study will develop further a number of recent Implementation Studies: 

During 2019-21, this project will provide foundational infrastructure building blocks for the RD community, building on ELIXIR-supporting infrastructure and objectives:

  • Data analysis
  • Ensuring that data are findable, accessible, interoperable and reusable for humans and machines (FAIR)
  • Training
 ELIXIR Spain, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, EMBL-EBI, ELIXIR France, ELIXIR Slovenia, ELIXIR Switzerland, ELIXIR UK

This Study will build on recent developments across the RD community by aligning and securely interconnecting existing international infrastructures (RD-Connect, European Genome-phenome Archive (EGA), and tranSMART) with the general ELIXIR infrastructure. Tasks will develop upon services provided by ELIXIR Nodes and international standards such as those from the Global Alliance for Genomics and Health (GA4GH).

This proposal will also build on the FAIR metrics described by Wilkinson et al. to establish a framework for RD data FAIRification by providing RD-specific recommendations and FAIRness scores. This framework will be evaluated through the FAIRNess estimation of different key RD resources such as Orphanet and the RD-Connect platform. Once defined, the RD-adapted FAIR metrics will be prepared for IRDiRC recognition to serve the entire RD community.

The Study will develop further a number of recent Implementation Studies: 

During 2019-21, this project will provide foundational infrastructure building blocks for the RD community, building on ELIXIR-supporting infrastructure and objectives:

  • Data analysis
  • Ensuring that data are findable, accessible, interoperable and reusable for humans and machines (FAIR)
  • Training
 ELIXIR Spain, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, EMBL-EBI, ELIXIR France, ELIXIR Slovenia, ELIXIR Switzerland, ELIXIR UK

RD-Connect is a platform for rare disease research that includes integrated analysis tools for whole human genome and exome data. The platform distributes variant calls, deposited at the European Genome-phenome Archive (EGA) while still controlled by RD-Connect, thereby avoiding duplication of processed data-sets and save network bandwidth.

This Implementation Study is a pilot of a robust, real-time visualization of genomic data, using the GA4GH htsget API to integrate data into the IGV genome browser within the RD-Connect genome-phonome analysis platform. The is currently used by more that 450 researchers, clinicians and bioinformaticians across 130 establisments in 15 countries. Visualisation of these data adds value to the RD-Connect service which could be offered to the wider EGA user community.

The study has been completed, the end report is available through the ELIXIR F1000R channel

Other Implementation Studies: 

 ELIXIR Spain, EMBL-EBI